@rbalchii/anchor-engine 4.7.0

package/engine/dist/services/ingest/github-ingest-service.js

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+/**
+ * GitHub Repository Ingestion Service (Standard 115)
+ *
+ * Downloads GitHub repository tarballs, extracts source files,
+ * and ingests them into the Anchor knowledge graph.
+ */
+import { gotScraping } from 'got-scraping';
+import * as tar from 'tar';
+import * as fs from 'fs';
+import * as path from 'path';
+import * as os from 'os';
+import { db } from '../../core/db.js';
+import { AtomizerService } from './atomizer-service.js';
+import { AtomicIngestService } from './ingest-atomic.js';
+// File exclusion patterns (Standard 115, Section 3.3)
+const EXCLUDE_PATTERNS = [
+    'node_modules/',
+    '.git/',
+    'dist/',
+    'build/',
+    'target/',
+    'vendor/',
+    '.bin',
+    '.exe',
+    '.dll',
+    '.so',
+    '.dylib',
+    '.png',
+    '.jpg',
+    '.jpeg',
+    '.gif',
+    '.svg',
+    '.ico',
+    '.pdf',
+    '.doc',
+    '.docx',
+    '.lock', // package-lock.json, Cargo.lock, etc.
+];
+// Language detection by extension
+const LANGUAGE_MAP = {
+    '.ts': 'typescript',
+    '.tsx': 'typescript',
+    '.js': 'javascript',
+    '.jsx': 'javascript',
+    '.py': 'python',
+    '.rs': 'rust',
+    '.go': 'go',
+    '.java': 'java',
+    '.cpp': 'cpp',
+    '.cc': 'cpp',
+    '.cxx': 'cpp',
+    '.h': 'cpp',
+    '.hpp': 'cpp',
+    '.c': 'c',
+    '.cs': 'csharp',
+    '.rb': 'ruby',
+    '.php': 'php',
+    '.swift': 'swift',
+    '.kt': 'kotlin',
+    '.scala': 'scala',
+    '.ex': 'elixir',
+    '.exs': 'elixir',
+    '.erl': 'erlang',
+    '.hs': 'haskell',
+    '.clj': 'clojure',
+    '.cljs': 'clojure',
+    '.ml': 'ocaml',
+    '.fs': 'fsharp',
+    '.vue': 'vue',
+    '.svelte': 'svelte',
+    '.html': 'html',
+    '.css': 'css',
+    '.scss': 'scss',
+    '.sass': 'sass',
+    '.less': 'less',
+    '.json': 'json',
+    '.yaml': 'yaml',
+    '.yml': 'yaml',
+    '.toml': 'toml',
+    '.md': 'markdown',
+    '.sql': 'sql',
+    '.sh': 'shell',
+    '.bash': 'shell',
+    '.zsh': 'shell',
+    '.ps1': 'powershell',
+    '.dockerfile': 'dockerfile',
+    '.xml': 'xml',
+    '.lua': 'lua',
+    '.r': 'r',
+    '.R': 'r',
+};
+export class GitHubIngestService {
+    atomizer;
+    atomicIngest;
+    constructor() {
+        this.atomizer = new AtomizerService();
+        this.atomicIngest = new AtomicIngestService();
+    }
+    /**
+     * Parse GitHub URL into components
+     * Supports:
+     * - https://github.com/{owner}/{repo}
+     * - https://github.com/{owner}/{repo}/tree/{branch}
+     */
+    parseGitHubUrl(url) {
+        const parsed = new URL(url);
+        const parts = parsed.pathname.split('/').filter(Boolean);
+        if (parts.length < 2) {
+            throw new Error(`Invalid GitHub URL: ${url}`);
+        }
+        const owner = parts[0];
+        const repo = parts[1].replace('.git', '');
+        // Detect branch from /tree/{branch}
+        let branch = 'main';
+        if (parts[2] === 'tree' && parts[3]) {
+            branch = parts[3];
+        }
+        else if (parts[2] && !parts[2].includes('.')) {
+            // Could be a branch without /tree/
+            branch = parts[2];
+        }
+        return { owner, repo, branch };
+    }
+    /**
+     * Download tarball from GitHub API
+     * Returns path to downloaded tarball
+     */
+    async downloadTarball(owner, repo, branch, token) {
+        const tarballUrl = `https://api.github.com/repos/${owner}/${repo}/tarball/${branch}`;
+        const headers = {
+            'Accept': 'application/vnd.github.v3+json',
+            'User-Agent': 'anchor-engine-node',
+        };
+        if (token) {
+            headers['Authorization'] = `token ${token}`;
+        }
+        const tempDir = fs.mkdtempSync(path.join(os.tmpdir(), 'github-ingest-'));
+        const tarballPath = path.join(tempDir, 'repo.tar.gz');
+        console.log(`[GitHub] Downloading tarball: ${tarballUrl}`);
+        // Retry logic (up to 3 times with exponential backoff)
+        let lastError = null;
+        for (let attempt = 1; attempt <= 3; attempt++) {
+            try {
+                // Use native fetch for better redirect handling
+                const response = await fetch(tarballUrl, {
+                    headers,
+                    redirect: 'follow', // Follow redirects automatically
+                });
+                if (!response.ok) {
+                    const errorText = await response.text();
+                    throw new Error(`GitHub API error: ${response.status} ${response.statusText} - ${errorText}`);
+                }
+                // Check Content-Type - should be application/octet-stream or application/x-gzip
+                const contentType = response.headers.get('content-type');
+                if (contentType && contentType.includes('application/json')) {
+                    // GitHub returned an error response as JSON instead of tarball
+                    const errorData = await response.json();
+                    throw new Error(`GitHub returned JSON instead of tarball: ${JSON.stringify(errorData)}`);
+                }
+                // Check rate limit headers
+                const remaining = response.headers.get('x-ratelimit-remaining');
+                const reset = response.headers.get('x-ratelimit-reset');
+                if (remaining && parseInt(remaining) < 10) {
+                    console.warn(`[GitHub] Rate limit warning: ${remaining} requests remaining. Resets at ${reset}`);
+                }
+                // Get the buffer
+                const arrayBuffer = await response.arrayBuffer();
+                const buffer = Buffer.from(arrayBuffer);
+                // Verify it's a valid tarball (should be > 1KB)
+                if (buffer.length < 1024) {
+                    throw new Error(`Downloaded file too small (${buffer.length} bytes). Likely an API error.`);
+                }
+                fs.writeFileSync(tarballPath, buffer);
+                console.log(`[GitHub] Downloaded ${buffer.length} bytes to ${tarballPath}`);
+                return tarballPath;
+            }
+            catch (error) {
+                lastError = error;
+                console.warn(`[GitHub] Download attempt ${attempt} failed: ${error.message}`);
+                if (attempt < 3) {
+                    const delay = Math.pow(2, attempt - 1) * 1000; // 1s, 2s, 4s
+                    console.log(`[GitHub] Retrying in ${delay}ms...`);
+                    await new Promise(resolve => setTimeout(resolve, delay));
+                }
+            }
+        }
+        throw lastError || new Error('Failed to download tarball after 3 attempts');
+    }
+    /**
+     * Extract tarball to temporary directory
+     * Returns path to extracted directory
+     */
+    async extractTarball(tarballPath) {
+        const extractDir = path.join(path.dirname(tarballPath), 'extracted');
+        fs.mkdirSync(extractDir, { recursive: true });
+        console.log(`[GitHub] Extracting tarball to ${extractDir}`);
+        await tar.x({
+            file: tarballPath,
+            cwd: extractDir,
+            strip: 1, // Remove top-level directory (owner-repo-hash)
+        });
+        return extractDir;
+    }
+    /**
+     * Check if file is binary by checking for null bytes
+     */
+    async isBinaryFile(filePath) {
+        try {
+            const fd = await fs.promises.open(filePath, 'r');
+            const buffer = Buffer.alloc(8192); // Check first 8KB
+            await fd.read(buffer, 0, 8192, 0);
+            await fd.close();
+            // Check for null bytes (common in binary files)
+            for (let i = 0; i < buffer.length; i++) {
+                if (buffer[i] === 0) {
+                    return true;
+                }
+            }
+            return false;
+        }
+        catch {
+            return true; // Assume binary if we can't read it
+        }
+    }
+    /**
+     * Detect programming language from file extension
+     */
+    detectLanguage(filePath) {
+        const ext = path.extname(filePath).toLowerCase();
+        const basename = path.basename(filePath).toLowerCase();
+        // Check for special filenames first
+        if (basename === 'dockerfile')
+            return 'dockerfile';
+        if (basename === 'makefile')
+            return 'makefile';
+        return LANGUAGE_MAP[ext] || 'unknown';
+    }
+    /**
+     * Check if file should be excluded
+     */
+    shouldExclude(filePath) {
+        const relativePath = filePath.toLowerCase();
+        return EXCLUDE_PATTERNS.some(pattern => {
+            if (pattern.startsWith('.')) {
+                // Extension check
+                return relativePath.endsWith(pattern);
+            }
+            else {
+                // Directory/path check
+                return relativePath.includes(pattern);
+            }
+        });
+    }
+    /**
+     * Walk directory and return list of source files
+     */
+    async walkDirectory(dir, baseDir = dir) {
+        const files = [];
+        try {
+            const entries = await fs.promises.readdir(dir, { withFileTypes: true });
+            for (const entry of entries) {
+                const fullPath = path.join(dir, entry.name);
+                // Skip excluded paths
+                if (this.shouldExclude(fullPath)) {
+                    continue;
+                }
+                if (entry.isDirectory()) {
+                    const subFiles = await this.walkDirectory(fullPath, baseDir);
+                    files.push(...subFiles);
+                }
+                else if (entry.isFile()) {
+                    // Skip binary files
+                    const isBinary = await this.isBinaryFile(fullPath);
+                    if (!isBinary) {
+                        files.push(fullPath);
+                    }
+                }
+            }
+        }
+        catch (error) {
+            console.warn(`[GitHub] Error walking directory ${dir}: ${error.message}`);
+        }
+        return files;
+    }
+    /**
+     * Register a new GitHub repository in the database
+     */
+    async registerRepo(url, bucket) {
+        const { owner, repo, branch } = this.parseGitHubUrl(url);
+        // Generate unique ID
+        const id = `github_${owner}_${repo}_${branch}`;
+        console.log(`[GitHub] Registering repo: ${owner}/${repo} (branch: ${branch})`);
+        // Insert or update record
+        await db.run(`INSERT INTO github_repos (id, owner, repo, branch, bucket, github_url, last_sync_status)
+       VALUES ($1, $2, $3, $4, $5, $6, 'pending')
+       ON CONFLICT (id) DO UPDATE SET
+         bucket = $5,
+         github_url = $6,
+         updated_at = CURRENT_TIMESTAMP`, [id, owner, repo, branch, bucket, url]);
+        return {
+            id,
+            owner,
+            repo,
+            branch,
+            bucket,
+            github_url: url,
+            total_files: 0,
+            total_atoms: 0,
+            total_size_bytes: 0,
+        };
+    }
+    /**
+     * Sync a repository (download, extract, ingest)
+     */
+    async syncRepo(repoId) {
+        const startTime = Date.now();
+        // Get repo record
+        const result = await db.run(`SELECT * FROM github_repos WHERE id = $1`, [repoId]);
+        if (!result.rows || result.rows.length === 0) {
+            throw new Error(`Repository not found: ${repoId}`);
+        }
+        const repo = result.rows[0];
+        console.log(`[GitHub] Syncing ${repo.owner}/${repo.repo} (bucket: ${repo.bucket})`);
+        // Update status to in_progress
+        await db.run(`UPDATE github_repos SET last_sync_status = 'in_progress', last_error = NULL WHERE id = $1`, [repoId]);
+        try {
+            // Get GitHub token from env (optional)
+            const token = process.env.GITHUB_TOKEN;
+            // Download tarball
+            const tarballPath = await this.downloadTarball(repo.owner, repo.repo, repo.branch, token);
+            // Extract tarball
+            const extractDir = await this.extractTarball(tarballPath);
+            // Walk directory and get files
+            const files = await this.walkDirectory(extractDir);
+            console.log(`[GitHub] Found ${files.length} source files`);
+            // Quarantine old atoms from this repo (Standard 115, Section 4.5)
+            await this.quarantineOldAtoms(repoId);
+            // Ingest each file
+            let filesIngested = 0;
+            let totalAtoms = 0;
+            let totalMolecules = 0;
+            let totalSize = 0;
+            for (const file of files) {
+                try {
+                    const content = await fs.promises.readFile(file, 'utf8');
+                    const relativePath = path.relative(extractDir, file);
+                    // Construct source path: github:{owner}/{repo}/{filepath}
+                    const sourcePath = `github:${repo.owner}/${repo.repo}/${relativePath}`;
+                    console.log(`[GitHub] Ingesting: ${relativePath}`);
+                    // Atomize
+                    const atomizeResult = await this.atomizer.atomize(content, sourcePath, 'external');
+                    // Skip if transient data detected
+                    if (!atomizeResult) {
+                        console.log(`[GitHub] ⚠️ SKIP: ${relativePath} - Transient data`);
+                        continue;
+                    }
+                    const { compound, molecules, atoms } = atomizeResult;
+                    // Ingest
+                    await this.atomicIngest.ingestResult(compound, molecules, atoms, [repo.bucket]);
+                    filesIngested++;
+                    totalAtoms += atoms.length;
+                    totalMolecules += molecules.length;
+                    totalSize += Buffer.byteLength(content, 'utf8');
+                    // Yield to event loop periodically
+                    if (filesIngested % 10 === 0) {
+                        await new Promise(resolve => setImmediate(resolve));
+                    }
+                }
+                catch (error) {
+                    console.warn(`[GitHub] Failed to ingest ${file}: ${error.message}`);
+                }
+            }
+            // Cleanup temp directory
+            await fs.promises.rm(path.dirname(tarballPath), { recursive: true, force: true });
+            // Update repo record
+            await db.run(`UPDATE github_repos SET
+          last_synced_at = CURRENT_TIMESTAMP,
+          last_sync_status = 'success',
+          total_files = $1,
+          total_atoms = $2,
+          total_size_bytes = $3,
+          updated_at = CURRENT_TIMESTAMP
+         WHERE id = $4`, [filesIngested, totalAtoms, totalSize, repoId]);
+            const duration = Date.now() - startTime;
+            console.log(`[GitHub] Sync complete: ${filesIngested} files, ${totalAtoms} atoms in ${(duration / 1000).toFixed(1)}s`);
+            return {
+                files_ingested: filesIngested,
+                atoms_created: totalAtoms,
+                molecules_created: totalMolecules,
+                total_size_bytes: totalSize,
+                duration_ms: duration,
+            };
+        }
+        catch (error) {
+            // Update status to failed
+            await db.run(`UPDATE github_repos SET last_sync_status = 'failed', last_error = $1 WHERE id = $2`, [error.message, repoId]);
+            throw error;
+        }
+    }
+    /**
+     * Quarantine old atoms from a repository
+     */
+    async quarantineOldAtoms(repoId) {
+        const result = await db.run(`SELECT owner, repo FROM github_repos WHERE id = $1`, [repoId]);
+        if (!result.rows || result.rows.length === 0)
+            return;
+        const { owner, repo } = result.rows[0];
+        const sourcePrefix = `github:${owner}/${repo}/`;
+        console.log(`[GitHub] Quarantining old atoms with source_path LIKE '${sourcePrefix}%'`);
+        // Add #quarantined tag to old atoms
+        await db.run(`UPDATE atoms SET
+        tags = array_cat(COALESCE(tags, '{}'), ARRAY['#quarantined']),
+        provenance = 'quarantine'
+       WHERE source_path LIKE $1`, [`${sourcePrefix}%`]);
+    }
+    /**
+     * List all registered GitHub repositories
+     */
+    async listRepos() {
+        const result = await db.run(`SELECT * FROM github_repos ORDER BY created_at DESC`);
+        return result.rows || [];
+    }
+    /**
+     * Remove a repository from the registry
+     */
+    async removeRepo(repoId) {
+        // First, quarantine all atoms from this repo
+        const result = await db.run(`SELECT owner, repo FROM github_repos WHERE id = $1`, [repoId]);
+        let quarantinedCount = 0;
+        if (result.rows && result.rows.length > 0) {
+            const { owner, repo } = result.rows[0];
+            const sourcePrefix = `github:${owner}/${repo}/`;
+            const updateResult = await db.run(`UPDATE atoms SET
+          tags = array_cat(COALESCE(tags, '{}'), ARRAY['#quarantined']),
+          provenance = 'quarantine'
+         WHERE source_path LIKE $1`, [`${sourcePrefix}%`]);
+            quarantinedCount = updateResult.rowCount || 0;
+        }
+        // Delete repo record
+        await db.run(`DELETE FROM github_repos WHERE id = $1`, [repoId]);
+        return quarantinedCount;
+    }
+    /**
+     * Fetch full commit history from GitHub API and ingest as searchable molecules.
+     * Each commit becomes its own paragraph: sha, author, date, message, files changed.
+     * The entire history is ingested as one compound: github:{owner}/{repo}/commit-history.md
+     */
+    async ingestGitHistory(owner, repo, branch, bucket, token) {
+        const headers = {
+            'Accept': 'application/vnd.github.v3+json',
+            'User-Agent': 'anchor-engine-node',
+        };
+        if (token)
+            headers['Authorization'] = `token ${token}`;
+        const commits = [];
+        let page = 1;
+        const PER_PAGE = 100;
+        console.log(`[GitHub] Fetching commit history for ${owner}/${repo} (branch: ${branch})`);
+        while (true) {
+            const url = `https://api.github.com/repos/${owner}/${repo}/commits?sha=${branch}&per_page=${PER_PAGE}&page=${page}`;
+            const res = await fetch(url, { headers });
+            if (!res.ok) {
+                console.warn(`[GitHub] Commits API error ${res.status} on page ${page} — stopping`);
+                break;
+            }
+            const data = await res.json();
+            if (!Array.isArray(data) || data.length === 0)
+                break;
+            for (const c of data) {
+                const sha = (c.sha || '').slice(0, 12);
+                const author = c.commit?.author?.name || c.author?.login || 'unknown';
+                const date = c.commit?.author?.date || '';
+                const message = (c.commit?.message || '').trim();
+                const filesLine = Array.isArray(c.files)
+                    ? c.files.map((f) => `  ${f.status[0].toUpperCase()} ${f.filename} (+${f.additions} -${f.deletions})`).join('\n')
+                    : '';
+                commits.push(`## ${sha} — ${date}\nAuthor: ${author}\n\n${message}${filesLine ? '\n\nFiles:\n' + filesLine : ''}`);
+            }
+            console.log(`[GitHub] Fetched page ${page} (${data.length} commits, total so far: ${commits.length})`);
+            // Check Link header for next page
+            const linkHeader = res.headers.get('link') || '';
+            if (!linkHeader.includes('rel="next"'))
+                break;
+            page++;
+            // Yield to event loop between pages
+            await new Promise(resolve => setImmediate(resolve));
+        }
+        if (commits.length === 0) {
+            console.log(`[GitHub] No commits found for ${owner}/${repo}`);
+            return 0;
+        }
+        const historyContent = `# Git History: ${owner}/${repo} (${branch})\n\nTotal commits: ${commits.length}\n\n---\n\n${commits.join('\n\n---\n\n')}`;
+        const sourcePath = `github:${owner}/${repo}/commit-history.md`;
+        console.log(`[GitHub] Ingesting ${commits.length} commits as ${sourcePath}`);
+        const atomizeResult = await this.atomizer.atomize(historyContent, sourcePath, 'external');
+        if (atomizeResult) {
+            const { compound, molecules, atoms } = atomizeResult;
+            await this.atomicIngest.ingestResult(compound, molecules, atoms, [bucket, 'git-history']);
+        }
+        return commits.length;
+    }
+    async getRateLimitStatus() {
+        const token = process.env.GITHUB_TOKEN;
+        const url = token
+            ? 'https://api.github.com/rate_limit'
+            : 'https://api.github.com/rate_limit';
+        try {
+            const headers = {
+                'Accept': 'application/vnd.github.v3+json',
+                'User-Agent': 'anchor-engine-node',
+            };
+            if (token) {
+                headers['Authorization'] = `token ${token}`;
+            }
+            const response = await gotScraping(url, { headers });
+            const data = JSON.parse(response.body);
+            const core = data.resources.core;
+            return {
+                limit: core.limit,
+                remaining: core.remaining,
+                reset_at: new Date(core.reset * 1000).toISOString(),
+                authenticated: !!token,
+            };
+        }
+        catch (error) {
+            console.error(`[GitHub] Failed to get rate limit: ${error.message}`);
+            // Return conservative defaults
+            return {
+                limit: 60,
+                remaining: 0,
+                reset_at: new Date(Date.now() + 3600000).toISOString(),
+                authenticated: false,
+            };
+        }
+    }
+}
+//# sourceMappingURL=github-ingest-service.js.map

package/engine/dist/services/ingest/github-ingest-service.js.map

@@ -0,0 +1 @@
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package/engine/dist/services/ingest/ingest-atomic.d.ts

@@ -0,0 +1,16 @@
+import { Atom, Molecule, Compound } from '../../types/atomic.js';
+export declare class AtomicIngestService {
+    ingestResult(compound: Compound, molecules: Molecule[], atoms: Atom[], buckets?: string[]): Promise<void>;
+    private _ingestResultInTransaction;
+    private batchWriteAtoms;
+    private batchWriteTags;
+    private batchWriteMolecules;
+    private batchWriteEdges;
+    private batchWriteCompounds;
+    private batchWriteMemory;
+    private batchWriteAtomPositions;
+    private flushAtomPositionsBatch;
+    private zeroVector;
+    private generateHash;
+}
+//# sourceMappingURL=ingest-atomic.d.ts.map

package/engine/dist/services/ingest/ingest-atomic.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"ingest-atomic.d.ts","sourceRoot":"","sources":["../../../src/services/ingest/ingest-atomic.ts"],"names":[],"mappings":"AAEA,OAAO,EAAE,IAAI,EAAE,QAAQ,EAAE,QAAQ,EAAE,MAAM,uBAAuB,CAAC;AAGjE,qBAAa,mBAAmB;IAEtB,YAAY,CACd,QAAQ,EAAE,QAAQ,EAClB,SAAS,EAAE,QAAQ,EAAE,EACrB,KAAK,EAAE,IAAI,EAAE,EACb,OAAO,GAAE,MAAM,EAAa;YAsElB,0BAA0B;YA6D1B,eAAe;YAqCf,cAAc;YAuCd,mBAAmB;YAoFnB,eAAe;YAqBf,mBAAmB;YAyDnB,gBAAgB;YA6GhB,uBAAuB;YA8BvB,uBAAuB;IAkBrC,OAAO,CAAC,UAAU;IAIlB,OAAO,CAAC,YAAY;CAWvB"}